rs6019102

Variant names:

• chr20-37524942-C-T
• rs6019102
• NM_006698.4:c.-177+2851G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_006698.4(BLCAP):​c.-177+2851G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.744 in 152,154 control chromosomes in the GnomAD database, including 42,525 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.74 (42525 hom., cov: 32)
• Consequence: BLCAP NM_006698.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.310
• Publications: 5 publications found

Genes affected

BLCAP (HGNC:1055): (BLCAP apoptosis inducing factor) This gene encodes a protein that reduces cell growth by stimulating apoptosis. Alternative splicing and the use of alternative promoters result in multiple transcript variants encoding the same protein. This gene is imprinted in brain where different transcript variants are expressed from each parental allele. Transcript variants initiating from the upstream promoter are expressed preferentially from the maternal allele, while transcript variants initiating downstream of the interspersed NNAT gene (GeneID:4826) are expressed from the paternal allele. Transcripts at this locus may also undergo A to I editing, resulting in amino acid changes at three positions in the N-terminus of the protein. [provided by RefSeq, Nov 2015]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.848 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BLCAP	NM_006698.4	c.-177+2851G>A		intron_variant	Intron 1 of 1	ENST00000373537.7	NP_006689.1
BLCAP	NM_001167820.2	c.-310+2851G>A		intron_variant	Intron 1 of 2		NP_001161292.1
BLCAP	NM_001167821.2	c.-177+2689G>A		intron_variant	Intron 1 of 1		NP_001161293.1
BLCAP	NM_001167822.3	c.-177+2632G>A		intron_variant	Intron 1 of 1		NP_001161294.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BLCAP	ENST00000373537.7	c.-177+2851G>A		intron_variant	Intron 1 of 1	1	NM_006698.4	ENSP00000362637.2

Frequencies

GnomAD3 genomes AF: 0.744 AC: 113171 AN: 152036 Hom.: 42489 Cov.: 32

Gnomad AFR AF: 0.689

Gnomad AMI AF: 0.640

Gnomad AMR AF: 0.694

Gnomad ASJ AF: 0.592

Gnomad EAS AF: 0.869

Gnomad SAS AF: 0.805

Gnomad FIN AF: 0.894

Gnomad MID AF: 0.585

Gnomad NFE AF: 0.764

Gnomad OTH AF: 0.678

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.744 AC: 113259 AN: 152154 Hom.: 42525 Cov.: 32 AF XY: 0.750 AC XY: 55795 AN XY: 74396

African (AFR) AF: 0.688 AC: 28565 AN: 41492

American (AMR) AF: 0.694 AC: 10618 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.592 AC: 2052 AN: 3468

East Asian (EAS) AF: 0.869 AC: 4483 AN: 5160

South Asian (SAS) AF: 0.805 AC: 3883 AN: 4822

European-Finnish (FIN) AF: 0.894 AC: 9479 AN: 10604

Middle Eastern (MID) AF: 0.585 AC: 172 AN: 294

European-Non Finnish (NFE) AF: 0.765 AC: 51985 AN: 67994

Other (OTH) AF: 0.681 AC: 1438 AN: 2112

Alfa AF: 0.756 Hom.: 5442

Bravo AF: 0.723

Asia WGS AF: 0.833 AC: 2892 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	6.9
DANN	Benign	0.60
PhyloP100		-0.31
PromoterAI		-0.019	Neutral
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs6019102; hg19: chr20-36153344;